Protein-induced photophysical changes to the amyloid indicator dye thioflavin T Leslie S. Wolfe1, Matthew F. Calabrese1, Abhinav Nath1, Dorottya V. Blaho, Andrew D. Miranker2, and Yong Xiong2 Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114 Edited by José N. Onuchic, University of California San Diego, La Jolla, CA, and approved August 4, 2010 (received for review March 8, 2010) The small molecule thioflavin T (ThT) is a defining probe for the spectrum and an increase in quantum yield (Fig. 1D, Inset, and identification and mechanistic study of amyloid fiber formation. Fig. S1) (9). ThT in protic solvents principally absorbs at As such, ThT is fundamental to investigations of serious diseases 340 nm with an emission maximum at 445 nm. Upon binding amy- such as Alzheimer’s disease, Parkinson disease, and type II diabetes. loid-like states, a peak at approximately 440 nm becomes domi- For each disease, a different protein undergoes conformational nant with the fluorescent emission maximum shifted to 480 nm. conversion to a β-sheet rich fiber. The fluorescence of ThT exhibits This is accompanied by a strong enhancement of the fluorescence. an increase in quantum yield upon binding these fibers. Despite These changes are collectively referred to as a “ThT positive” its widespread use, the structural basis for binding specificity and state. Despite the extensive use of ThT as an indicator dye, the for the changes to the photophysical properties of ThT remain structural basis of its interactions with amyloid and amyloid-like poorly understood. Here, we report the co-crystal structures of states remains poorly understood (10). ThT with two alternative states of β-2 microglobulin (β2m); one Recently, we reported the crystal structure of an amyloid-like monomeric, the other an amyloid-like oligomer. In the latter, the oligomer of β-2 microglobulin (β2m) (11). β2m is the 12 kDa light dye intercalates between β-sheets orthogonal to the β-strands. chain noncovalently associated with the Class I Major Histocom- Importantly, the fluorophore is bound in such a manner that a patibility complex (MHC) (12). It directs proper folding and photophysically relevant torsion is limited to a range of angles cell-surface expression of MHC. As part of normal cellular turn- generally associated with low, not high, quantum yield. Quantum over, β2m is released to the serum and catabolized by the kidneys. mechanical assessment of the fluorophore shows the electronic In patients on long-term hemodialysis therapy, serum levels are BIOPHYSICS AND distribution to be strongly stabilized by aromatic interactions with β elevated and 2m deposits as amyloid plaques. This conversion COMPUTATIONAL BIOLOGY the protein. Monomeric β2m gives little increase in ThT fluorescence can be induced in vitro by exposure to Cu2þ. Under such condi- despite showing three fluorophores, at two binding sites, in config- tions, β2m self-associates to populate closed amyloid-like oligo- urations generally associated with high quantum yield. Our efforts mers prior to mature fiber formation (13). These nonfibrillar, fundamentally extend existing understanding about the origins amyloid-like states are ThT positive in solution yet are amenable of amyloid-induced photophysical changes. Specifically, the β-sheet to crystallization, providing a unique opportunity for structural interface that characterizes amyloid acts both sterically and analysis (11, 13). In this work, we determine the crystal structures CHEMISTRY electronically to stabilize the fluorophore’s ground state electronic of ThT bound to both amyloid-like and nonamyloid states of distribution. By preventing the fluorophore from adopting its β2m. These structures allow for an interrogation of the structural preferred excited state configuration, nonradiative relaxation basis of ThT fluorescence enhancements as well as a direct com- pathways are minimized and quantum yield is increased. parison of the structures of ThT positive and negative states. Alzheimer’s ∣ beta-2 microglobulin ∣ Parkinson ∣ TICT ∣ photophysics Results In order to investigate the structural basis of ThT–amyloid inter- he conversion of a normally soluble protein into fibrillar actions, we first prepared two sets of β2m crystals in the presence β2 β2 2þ β2 Taggregates is of central importance to a range of diseases ( mholo) and absence ( mapo) of its metal ligand, Cu . mapo is including Alzheimer’s disease, Parkinson disease, and type II monomeric and well behaved under physiological solution condi- diabetes (1). Despite the involvement of distinct proteins in each tions. In contrast, the holo state undergoes conformational of these conditions, the fibers formed share a common set of changes resulting in the formation of a hexameric species (11, 13). β2 structural and biophysical properties, which define them as amy- Long-term incubation at 37 °C results in aggregation of mholo β2 loid. Amyloid fibers are homopolymeric, noncovalent assemblies, but not mapo (14). Both sets of crystals were prepared in the pre- which present morphologically as twisted sets of unbranched sence of 5 mM ThT. We then directly analyzed the fluorescence filaments. These filaments are composed of two or more β-sheets properties of the crystals. This was followed by a determination whose strands run in a direction orthogonal to the long axis of of the structures of these two states at atomic resolution. : β2 the fiber (2, 3). This arrangement yields a characteristic cross-β Co-crystals of ThT mholo show strong fluorescence intensity : β2 pattern by X-ray diffraction, the presence of which represents when compared to ThT mapo. Crystals were imaged using both the gold standard for unequivocal identification of amyloid struc- near-UV (340 nm) and blue (440 nm) excitation light to enable ture (4, 5). As the routine use of diffraction has proven impractical for most Author contributions: L.S.W., M.F.C., A.N., and A.D.M. designed research; L.S.W., M.F.C., mechanistic studies of amyloid assembly, a considerable fraction A.N., D.V.B., A.D.M., and Y.X. performed research; L.S.W., A.N., A.D.M., and Y.X. analyzed of the publication record relies in whole or in part on the use of data; and L.S.W. and A.D.M. wrote the paper. benzothiazole dyes, most commonly thioflavin T (ThT) (Fig. 1A). The authors declare no conflict of interest. The breadth of their use includes histological, kinetic, imaging, This article is a PNAS Direct Submission. and structural studies (6, 7). ThT was first reported as a tool Data deposition: The atomic coordinates have been deposited in the Protein Databank, for detecting amyloid in ex vivo tissue samples in 1959, and this www.pdb.org (PDB ID codes 3MYZ and 3MZT). interaction was suggested to be highly specific for amyloid-like 1L.S.W., M.F.C., and A.N. contributed equally to this work. structures (8). In later years, ThTwas characterized biophysically, 2To whom correspondence may be addressed. E-mail: [email protected] or resulting in its broad acceptance as a defining characteristic for [email protected]. the presence of amyloid (9). The changes in the fluorescent prop- This article contains supporting information online at www.pnas.org/lookup/suppl/ erties of ThTupon binding amyloid include a shift in its excitation doi:10.1073/pnas.1002867107/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1002867107 PNAS Early Edition ∣ 1of6 Downloaded by guest on September 26, 2021 A B structure (11) (chain D) gives an rmsd of 0.39 Å for the Cα posi- tions (Fig. 2B, Left). Thus, only modest deviations occur at the main chain. Most alterations are apparent at side chains within φ the interface, notably Gln8, Tyr10, and Tyr26. The maximum change appears limited to a rotamer change in Tyr10, which re- sults in a 2 Å shift in the position of the side-chain hydroxyl group (Fig. 2B, Left). If instead, alignment is performed using one of the pairs of chains that form the ThT binding pocket (chains D and E), a Cα rmsd of 0.69 Å is observed. In effect, chain E has moved approximately 1.5 Å away from chain D in comparison to our 30µm previously published structure (11) (Fig. 2B, Right). The change in the respective Cα positions reflects a simple increase in overall C D separation of the two subunits from one another in order to accommodate the fluorophore. We additionally note that the binding site is symmetric at this location. Indeed, two equivalent alternative conformations of ThTcan be modeled at this site with the benzothiazole ring stacking in parallel with one or the other of the Tyr10 residues (Fig. 3A and Figs. S3 and S4A). For both conformations, it is clear that ThT is buried within a β-sheet interface whose structure requires only modest alteration to ac- commodate the fluorophore. 30µm 30µm β2 In mholo, the binding pocket of the benzothiazole ring is well defined and dominated by the side chains of Tyr10 and Tyr26. Fig. 1. Visualization of ThT in protein crystals and aggregates. (A) The che- Contacts made by the benzothiazole ring include aromatic stack- mical structure of ThT. The angle ϕ is defined by the torsion angle between ing with Tyr10 in a configuration that includes cation–π and π–π the benzothiazole ring and the dimethylaminobenzene ring (20). ϕ ¼ 0 interactions (Fig. 3C). While density for the benzothiazole ring is corresponds to coplanarity of the two aromatic moieties. (B–D) False-color well defined, density for the dimethylaminobenzene portion of fluorescence images collected using blue-light (440 nm) excitation of human β2 β2 the fluorophore appears limited to a rotationally averaged con- islet amyloid fibers, mholo crystals and mapo crystals respectively. Relative ϕ intensity across panels B and D are directly comparable and use the same in- tribution along the -axis (Fig.